The goal of the proposed research is to address a critical gap in our understanding of the origin and evolution of gene copy number polymorphism within species. Preliminary work suggests copy number variation exists in Drosophila melanogaster; therefore, my training goals are to study the genetics and evolution of copy number variation in two species of Drosophila. The broad, long term objectives of the proposed research are (i) to characterize and quantify variation in gene copy gains and losses using microarray comparative genomic hybridization (aCGH), PCR, and real-time qPCR; (ii) to broadly define the genomic distribution for copy gains and losses using in situ hybridization of polytene chromosomes; (iii) to characterize new retroposed genes by taking advantages of sequence hallmarks associated with transposition; (iv) to quantify changes in the regulation of gene expression associated with duplicate copies by using real- time RT-qPCR; and (v) to characterize natural variation in gene copy number and expression using qPCR, RT-qPCR, and sequencing. These long-term objectives have been formulated to test specific predictions for genes with variable copies. [unreadable] [unreadable] [unreadable]